Nitrogen (N) saturation of upland forests has been assumed to be a substantial N source downstream. However, removal processes of N, including assimilation and denitrification in the downstream area, have not been clarified. To evaluate the N removal processes, nitrate (NO3−) and organic N concentrations, as well as nitrogen isotope ratio (δ15N) and oxygen isotope ratio (δ18O) of NO3− were measured along three rivers of Tatara River Basin, Japan where upland forests have already been N-saturated. Geographic information system (GIS) based topographical analysis was also conducted to evaluate the land use as urban area in relation to topography. In two of the three rivers, NO3− concentrations did not increase from upstream to downstream, despite the potential non-point N sources of urban areas. In another river, NO3− concentrations rather decreased. The values of δ15N and δ18O of NO3− and organic N concentrations suggested the presence of denitrification and assimilation over N pollutants in the river whose watersheds have a lower percentage of urban area. The lower percentage of urban area could be explained by the lower topographic index. This study concluded that the NO3− leaching from upland N-saturated forests was substantially assimilated or denitrified in the downstream area.